8BD3

Cryo-EM structure of the Photosystem II - LHCII supercomplex from Chlorella ohadi

This is a non-PDB format compatible entry.

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, FA (1, 7)	Chlorophyll a-b binding protein, chloroplastic	polymer	214	23060.1	2	UniProt (A0A2P6TPU9) Pfam (PF00504)	Chlorella ohadii
2	B, D, HA, JA, M... (2, 4, G, 9, q...)	Chlorophyll a-b binding protein, chloroplastic	polymer	222	23850.7	6	UniProt (A0A2P6TDA6) Pfam (PF00504)	Chlorella ohadii
3	C, E, GA, IA, T... (3, 5, N, 8, p...)	Chlorophyll a-b binding of LHCII	polymer	221	23847.9	6		Chlorella ohadii
4	EA, F (6, 0)	Chlorophyll a-b binding of LHCII	polymer	217	23455.5	2		Chlorella ohadii
5	G, KA (A, a)	Photosystem II protein D1	polymer	336	37230.3	2	UniProt (W8SIR2) Pfam (PF00124)	Chlorella ohadii
6	H, LA (B, b)	Photosystem II CP47 reaction center protein	polymer	504	55754.3	2	UniProt (W8TIK4) Pfam (PF00421)	Chlorella ohadii
7	I, MA (C, c)	Photosystem II CP43 reaction center protein	polymer	448	49161.1	2	UniProt (A0A076EAP1) Pfam (PF00421)	Chlorella ohadii	PSII 43 kDa protein,Protein CP-43
8	J, NA (D, d)	Photosystem II D2 protein	polymer	342	38459.9	2	UniProt (W8SYD4) Pfam (PF00124)	Chlorella ohadii
9	K, OA (E, e)	Cytochrome b559 subunit alpha	polymer	81	9204.3	2	UniProt (W8SU91) Pfam (PF00283) Pfam (PF00284)	Chlorella ohadii	PSII reaction center subunit V
10	L, PA (F, f)	Cytochrome b559 subunit beta	polymer	37	4262.1	2	UniProt (P56310) Pfam (PF00283)	Chlorella ohadii	PSII reaction center subunit VI
11	N, RA (H, h)	Photosystem II reaction center protein H	polymer	67	7223.4	2	UniProt (W8SIT0) Pfam (PF00737)	Chlorella ohadii
12	O, SA (I, i)	Photosystem II reaction center protein I	polymer	34	3871.5	2	UniProt (A0A5P4ND48) Pfam (PF02532)	Chlorella ohadii	PSII-I,PSII 4.8 kDa protein
13	P, TA (J, j)	Photosystem II reaction center protein J	polymer	38	3813.5	2	UniProt (W8TIH6) Pfam (PF01788)	Chlorella ohadii
14	Q, UA (K, k)	Photosystem II reaction center protein K	polymer	37	4140.0	2	UniProt (P56348) Pfam (PF02533)	Chlorella ohadii	PSII-K
15	R, VA (L, l)	Photosystem II reaction center protein L	polymer	37	4260.0	2	UniProt (P56339) Pfam (PF02419)	Chlorella ohadii	PSII-L
16	S, WA (M, m)	Photosystem II reaction center protein M	polymer	57	5621.9	2	UniProt (A0A5P4NAV9) Pfam (PF05151)	Chlorella ohadii
17	U, YA (O, o)	Chloroplast oxygen-evolving enhancer protein 1	polymer	240	25449.5	2	UniProt (A0A5P4NF37) Pfam (PF01716)	Chlorella ohadii
18	V, ZA (R, r)	Chlorophyll a b binding CP29	polymer	236	25803.7	2		Chlorella ohadii
19	AB, W (S, s)	Chlorophyll a b-binding CP26	polymer	257	27369.8	2		Chlorella ohadii
20	BB, X (T, t)	Photosystem II reaction center protein T	polymer	30	3476.2	2	UniProt (P56327) Pfam (PF01405)	Chlorella ohadii	PSII-T
21	CB, Y (V, v)	Photosystem II reaction center protein Ycf12	polymer	32	3319.0	2	UniProt (A0A076EAR3) Pfam (PF05969)	Chlorella ohadii
22	DB, Z (W, w)	Photosystem II reaction center W protein	polymer	60	6623.4	2		Chlorella ohadii
23	AA, EB (X, x)	Photosystem II reaction center protein X	polymer	37	3526.0	2		Chlorella ohadii
24	BA, FB (Y, y)	Multifunctional fusion protein	polymer	221	23864.0	2	UniProt (A0A2P6U5M3) Pfam (PF00504)	Chlorella ohadii
25	CA, GB (Z, z)	Photosystem II reaction center protein Z	polymer	62	6727.1	2	UniProt (W8SKL0) Pfam (PF01737)	Chlorella ohadii
26	DA, HB (U, u)	Chloroplast oxygen-evolving enhancer protein 3	polymer	144	15948.1	2	UniProt (A0A5P4NB29) Pfam (PF05757)	Chlorella ohadii
27	IB, KB (Q1, q1)	Chloroplast PsbY	polymer	34	3697.3	2	UniProt (A0A5P4NEE0)	Chlorella ohadii
28	JB, LB (P1, p1)	Chloroplast photosystem II 10 kDa protein	polymer	108	11657.3	2	UniProt (A0A5P4NAS4) Pfam (PF04725)	Chlorella ohadii
29	MB, NB (F1, f1)	Photosystem II oxygen evolving enhancer 2	polymer	188	20416.8	2		Chlorella ohadii
30	AF, AL, AQ, AR, BE... (5, N, 8, 9, 4...)	CHLOROPHYLL B	non-polymer		907.5	122	Chemie (CHL)
31	AC, AE, AG, AI, AJ... (1, 4, 6, C, D...)	CHLOROPHYLL A	non-polymer		893.5	270	Chemie (CLA)
32	ABA, AN, BO, CC, CG... (y, S, Y, 1, 6...)	(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL	non-polymer		568.9	36	Chemie (LUT)
33	AP, AX, BAA, BT, BW... (0, g, t, q, d...)	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE	non-polymer		723.0	44	Chemie (LHG)
34	AD, AH, BD, BP, BX... (2, A, 0, g, d...)	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE	non-polymer		787.2	86	Chemie (LMG)
35	IR, LE, UC, WW, YJ... (9, 4, 2, g, G...)	(3R)-beta,beta-caroten-3-ol	non-polymer		552.9	6	Chemie (RRX)
36	AK, AT, AZ, BBA, BN... (G, q, r, y, S...)	(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL	non-polymer		600.9	22	Chemie (NEX)
37	CT, CX, EK, EM, NR... (q, g, G, R, 9...)	(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL	non-polymer		600.9	8	Chemie (XAT)
38	BK, CP, DZ, EBA, EZ... (G, 0, r, y, s...)	1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL	non-polymer		795.1	24	Chemie (SQD)
39	ET, JG (a, A)	CA-MN4-O5 CLUSTER	non-polymer		339.8	2	Chemie (OEX)
40	FT, KG (a, A)	FE (II) ION	non-polymer		55.8	2	Chemie (FE2)
41	GT, HT, LG, MG (a, A)	CHLORIDE ION	non-polymer		35.5	4	Chemie (CL)
42	KT, QG, VV, YI (a, A, d, D)	PHEOPHYTIN A	non-polymer		871.2	4	Chemie (PHO)
43	AAA, CAA, CJ, EX, FBA... (t, v, D, h, z...)	BETA-CAROTENE	non-polymer		536.9	22	Chemie (BCR)
44	AW, DJ, QT, YG (d, D, a, A)	2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE	non-polymer		749.2	4	Chemie (PL9)
45	LV, MV, NV, OV, PI... (c, C)	DIGALACTOSYL DIACYL GLYCEROL (DGDG)	non-polymer		949.3	8	Chemie (DGD)
46	WV, ZI (d, D)	BICARBONATE ION	non-polymer		61.0	2	Chemie (BCT)
47	GW, KJ (e, E)	PROTOPORPHYRIN IX CONTAINING FE	non-polymer		616.5	2	Chemie (HEM)
48	JY, NK, OL, SV (r, K, R, c)	DODECYL-ALPHA-D-MALTOSIDE	non-polymer		510.6	4	Chemie (LMU)
49	ACA, ADA, BCA, CCA, DCA... (R, f1, S, T, Y...)	water	water		18.0	224	Chemie (HOH)

Sequence modifications

1, 7: 39 - 252 (UniProt: A0A2P6TPU9)

PDB	External Database	Details
Leu 195	Phe 719	conflict
Glu 225	Asp 749	conflict
Asn 250	Thr 774	conflict

2, 4, G, 9, q, g: 40 - 261 (UniProt: A0A2P6TDA6)

PDB	External Database	Details
Thr 74	Ser 64	conflict

M, m: -24 - 0 (PDB: 8BD3)
M, m: 1 - 32 (UniProt: A0A5P4NAV9)

Contents of the asymmetric unit

Polymers	Number of chains	66
	Total formula weight	1180984.5
Non-Polymers*	Number of molecules	672
	Total formula weight	542583.2
All*	Total formula weight	1723567.7

*Water molecules are not included.